CONTENTS OF THIS ARTICLE
From the left panel, click on “Designs” and choose the “Designs” option. This opens the Design Library, a repository of designs you have created or imported.
CREATING A NEW DESIGN
CREATING A DESIGN FROM SCRATCH
To create or import a design, click on the green “New Design” button. At the “Create New Design” page you have the following options: create a new design, upload an existing design, or load an example design.
Create a new design: Give your design a name (this is required), you can add a description and you have the option to add the design to a Project, then click "Save". This will take you to the Design editor. You will see a blank design with two bins and no more information.
Upload a design file from your computer: Give your design a name, you can add a description and add the design to a Project if you want to, then click on the “Choose File” button and select the file with your design. Supported format: JSON. Click Save.
UPLOADING A DESIGN IN CSV FORMAT
Before uploading it, the design information in your CSV file needs to be specified as:
Row 1: lists the names of the bins in the design
Other rows: variants of parts
Notice that all the parts must already exist in your "DNA Parts" library.
Once your file is ready, make sure to save it as a CSV file. To upload your design, from the header menu, go to your Designs library and click on "Upload", select your file and fill in the required information.
Then, click on "Submit" and you will be directed to the design editor where you can view your design. There are three possible scenarios around identifying the underlying DNA part represented by the part name when you upload via a CSV file:
If the part name matches only one part in your ‘DNA Parts’ library, the matched part will be inserted in the appropriate bin as specified in the CSV file. This is the common case that most users will want.
If the part name does not exist in your library, then an unmapped part (labeled by the red icon in front of the part name) will be inserted into your design. Before you can submit for assembly you will need to map the unmapped part to an actual part in your library by double-clicking on the part and selecting a part from the ‘DNA Parts’ library.
If multiple parts match the name, a part set that contains all of those parts will be created. If this is unintended the user will probably want to replace that part set in the design with just one of the parts that the set contains.
All parts that are labeled with the red icons do not exist in the "DNA Parts" library.
It is important to note that the following things are not supported in the CSV format:
SBOL icons are not supported in a design CSV import, so the user will need to set the icons manually after the upload.
You cannot create new sequences with this, so it is important to understand that the parts must already exist in the database.
Assembly method and parameter presets will also need to be set manually after the upload.
LOADING EXAMPLE DESIGNS
If you upload a design or load in one of the example designs, the Design editor will be loaded with parts that are defined in the uploaded design or the example design. To load an example design, follow the same procedure explained above, but this time select the assembly method you want to use.
The image below is an example of a Combinatorial Golden Gate design.
WORKING WITH DESIGNS
When working on the design Editor, there are several options you can change:
Add bins or rows: You can add a new part by adding a new bin, or add a variant of a part by adding a new row (this can only be done with a combinatorial design). Remember that this can be done by clicking on the "plus (+)" icon.
Assign a DNA part to a bin: You can associate one DNA part or more (if it's combinatorial) to a bin. To do this, double-click on the empty cell under the bin and a window will be displayed, where you can select the DNA part(s) you want to associate.
View and edit a bin's properties: Click on a bin to open the side panel with its information. There, you can change its name, direction, and overhang position, change the design rulesets, and add/remove a specific number of base pairs from the 3' or 5' endings.
To change the SBOL icon of a bin, click on the icon shown on the side panel and select an icon from the list.
View and edit a part's properties: You can obtain information about a part associated with a bin by either double-clicking on it to display the pop-up window or clicking and looking in the right panel, you can also obtain and edit information by clicking on a part associated (cells under each bin). This will show a side panel where you can add notes on the part, indicate your preferred overhangs, and indicate forced assembly strategies.
Forced Assembly Strategy: When editing the information of a part, you can indicate the forced assembly strategy by selecting from the list
Once you do this, the software will show a small colored square in the upper left corner of a part; you can obtain information by placing the cursor over it.
Notice duplicated parts: TeselaGen's software automatically detects duplicated parts and warns you by showing a yellow frame on the duplicated parts.
Add a direct synthesis firewall: One of the options shown in the side panel of a part allows you to add a direct synthesis firewall. In this case, you will be notified with a red frame shown on the corresponding part.
ANALYZING A DESIGN
Once your design is ready, you can use one of TeselaGen's most powerful tools by clicking on the "Submit for Assembly" option in the upper right corner of your screen.
You can check the status of your report on the notifications icon. In some cases, there are assembly errors, where the software will indicate the changes you need to do to successfully run the assembly analysis.
On the other hand, if the assembly successfully runs with no errors, you can access to it on the corresponding notification:
Another way to access the report is through the DNA Assembly Reports library:
A report contains the following sections:
Prebuilt constructs. These include the desired sequences that were already built and are available on the physical inventory.
Constructs. Final desired sequences to be built using the Design analysis.
Input sequences. Obtained from the input parts.
Input parts used in the analysis.
Assembly oligos that need to be synthesized.
Annealed oligos.
Digest linearized fragments that are going to be used in the assembly reaction.
Synthon sequences. Includes the sequences that need to be directly synthesized.
PCRs need to be run to generate the assembly pieces.
Assembly Pieces of DNA that will be in the final assembly reaction.
Assemblies. Includes assembly pieces that need to be combined to create each construct.